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Histone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

ABSTRACT: We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42374 | GEO | 2013/09/12

SECONDARY ACCESSION(S): PRJNA181207

REPOSITORIES: GEO

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Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when A549 is grown in spheroid cultures (2D control vs 3D untreated). EMT is efficiently induced only in the spheroid culture model.

2013-09-12 | GSE42373 | GEO

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress

Histone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha. The epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process that has been implicated in cancer progression and metastasis. Increasing evidence suggests that EMT is regulated and established by epigenetic reprogramming, however a systems-level mechanism describing how chromatin remodeling contributes to the phenotypic switch is not known. We have generated genome-wide maps of 18 histone modifications/variants and variants in both the epithelial and mesenchymal states and quantified patterns of epigenetic changes at gene and enhancer loci. Clusters of these patterns reveal that EMT-related genes and their proximal enhancers are regulated through coordinated patterns of chromatin activation and repression at both gene and enhancer loci. At the cellular level, the remodeling of gene loci translates into a modular protein interaction network that recapitulates EMT-related signaling. Moreover, differentially activated or repressed enhancers are associated with two non-overlapping sets of transcription factors. We propose a chromatin-mediated regulatory feedback loop model where the NFkappaB and AP-1 transcription factors (TFs) bind activated enhancers, that regulate EMT-related genes, which in turn activate signaling pathways upstream of these TFs.

2013-09-12 | E-GEOD-42374 | biostudies-arrayexpress

Gene expression analysis of glioblastoma spheroid cultures II

Project description:Microarray-based gene expression analysis identified genes differentially expressed in 10 glioblastoma spheroid cultures compared to a non-neoplastic spheroid culture isolated from the bulbus olfactorius In this study, a set of 10 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 17 093 transcripts, leading to the identification of differentially expressed genes compared to a non-neoplastic brain spheroid culture

2010-02-12 | E-GEOD-16666 | biostudies-arrayexpress

Gene expression analysis of glioblastoma spheroid cultures II

2010-02-13 | GSE16666 | GEO

Array CGH analysis of glioblastoma spheroid cultures

Project description:The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures. Keywords: Comparative genomic hybridization We performed array comparative genomic hybridization of spheroid cultures derived from 20 glioblastomas using as a reference DNA from healthy donors.

2010-05-14 | E-GEOD-14822 | biostudies-arrayexpress

Homo sapiens

Project description:Histone modification analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

| PRJNA181207 | ENA

Homo sapiens

Project description:Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

| PRJNA181206 | ENA

Expression data from TGFbeta-treated control or aPKC silenced A549 cells

Project description:Aberrant TGFbeta signalling is a hallmark of epithelial derived tumours. Signalling patterns can depend on the membrane trafficking and internalization of the TGFbeta receptors. Protein kinase C (PKC), particularly the atypical PKC isoforms, alter the trafficking of TGFbeta receptors and can alter TGFbeta induced gene expression. We used microarrays to detail the programme of gene expression underlying TGFbeta induction between control or aPKC silenced A549 cells. Control or aPKC silenced A549 cells were serum starved and treated with TGFbeta for 1 hour. Total RNA was extracted from untreated or TGFbeta treated cells after 8 and 24 hours and analyzed using Affymetrix microarrays. We sought to assess TGFbeta gene expression in aPKC silenced lung cancer cells, as we found that knockdown of aPKC extends TGFbeta signalling as assessed by phospho Smad2 levels. Furthermore, increased expression and oncogenic activity of aPKC (PKCiota) has been reported in lung cancer cells.

2011-01-29 | E-GEOD-26241 | biostudies-arrayexpress

Array CGH analysis of glioblastoma spheroid cultures

Project description:The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures. Keywords: Comparative genomic hybridization

2010-02-13 | GSE14822 | GEO

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